Starting phenix.real_space_refine on Fri Aug 22 13:56:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc4_40337/08_2025/8sc4_40337.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc4_40337/08_2025/8sc4_40337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sc4_40337/08_2025/8sc4_40337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc4_40337/08_2025/8sc4_40337.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sc4_40337/08_2025/8sc4_40337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc4_40337/08_2025/8sc4_40337.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 2335 2.51 5 N 579 2.21 5 O 599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3544 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3535 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 24, 'TRANS': 431} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.01, per 1000 atoms: 0.28 Number of scatterers: 3544 At special positions: 0 Unit cell: (88.803, 81.972, 67.4561, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 599 8.00 N 579 7.00 C 2335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 89.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 2 sheets defined 82.0% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 4.356A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 65 through 73 removed outlier: 4.048A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.570A pdb=" N GLY A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 145 through 173 removed outlier: 3.946A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.942A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 4.152A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 258 removed outlier: 4.439A pdb=" N ARG A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 280 Proline residue: A 271 - end of helix removed outlier: 3.680A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 340 through 372 Processing helix chain 'A' and resid 374 through 401 removed outlier: 3.666A pdb=" N SER A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 402 through 423 removed outlier: 3.580A pdb=" N ILE A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 removed outlier: 3.580A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 485 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.824A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 253 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.46 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1089 1.35 - 1.46: 929 1.46 - 1.58: 1575 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 3639 Sorted by residual: bond pdb=" N GLN A 241 " pdb=" CA GLN A 241 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.32e+00 bond pdb=" C07 MF8 A 601 " pdb=" N09 MF8 A 601 " ideal model delta sigma weight residual 1.358 1.317 0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C07 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.393 1.354 0.039 2.00e-02 2.50e+03 3.87e+00 bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.314 -0.033 2.00e-02 2.50e+03 2.78e+00 bond pdb=" C04 MF8 A 601 " pdb=" N05 MF8 A 601 " ideal model delta sigma weight residual 1.284 1.316 -0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 3634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 4628 1.21 - 2.43: 270 2.43 - 3.64: 45 3.64 - 4.86: 16 4.86 - 6.07: 4 Bond angle restraints: 4963 Sorted by residual: angle pdb=" C LEU A 180 " pdb=" N GLY A 181 " pdb=" CA GLY A 181 " ideal model delta sigma weight residual 119.94 122.86 -2.92 1.11e+00 8.12e-01 6.93e+00 angle pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " ideal model delta sigma weight residual 114.40 120.31 -5.91 2.30e+00 1.89e-01 6.60e+00 angle pdb=" N GLN A 241 " pdb=" CA GLN A 241 " pdb=" C GLN A 241 " ideal model delta sigma weight residual 111.07 108.38 2.69 1.07e+00 8.73e-01 6.34e+00 angle pdb=" C ASN A 374 " pdb=" N LEU A 375 " pdb=" CA LEU A 375 " ideal model delta sigma weight residual 120.54 123.86 -3.32 1.35e+00 5.49e-01 6.06e+00 angle pdb=" CA GLN A 241 " pdb=" C GLN A 241 " pdb=" O GLN A 241 " ideal model delta sigma weight residual 120.82 118.35 2.47 1.05e+00 9.07e-01 5.52e+00 ... (remaining 4958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 1938 14.28 - 28.56: 130 28.56 - 42.84: 35 42.84 - 57.12: 5 57.12 - 71.40: 2 Dihedral angle restraints: 2110 sinusoidal: 804 harmonic: 1306 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -47.29 -38.71 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" CA SER A 424 " pdb=" C SER A 424 " pdb=" N PRO A 425 " pdb=" CA PRO A 425 " ideal model delta harmonic sigma weight residual 180.00 -165.86 -14.14 0 5.00e+00 4.00e-02 8.00e+00 dihedral pdb=" CA ASN A 374 " pdb=" C ASN A 374 " pdb=" N LEU A 375 " pdb=" CA LEU A 375 " ideal model delta harmonic sigma weight residual -180.00 -165.96 -14.04 0 5.00e+00 4.00e-02 7.88e+00 ... (remaining 2107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 361 0.033 - 0.066: 159 0.066 - 0.099: 41 0.099 - 0.132: 12 0.132 - 0.165: 1 Chirality restraints: 574 Sorted by residual: chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA PRO A 286 " pdb=" N PRO A 286 " pdb=" C PRO A 286 " pdb=" CB PRO A 286 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA VAL A 126 " pdb=" N VAL A 126 " pdb=" C VAL A 126 " pdb=" CB VAL A 126 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 571 not shown) Planarity restraints: 613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " -1.308 2.00e-02 2.50e+03 6.51e-01 9.54e+03 pdb=" C03 MF8 A 601 " 1.075 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " -0.093 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " 0.035 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " -0.105 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " 0.321 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " -0.546 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " 0.721 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 406 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C MET A 406 " 0.041 2.00e-02 2.50e+03 pdb=" O MET A 406 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 407 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 182 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C THR A 182 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 182 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 183 " 0.013 2.00e-02 2.50e+03 ... (remaining 610 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 964 2.82 - 3.34: 3680 3.34 - 3.86: 5933 3.86 - 4.38: 6701 4.38 - 4.90: 11468 Nonbonded interactions: 28746 Sorted by model distance: nonbonded pdb=" OG SER A 196 " pdb=" OG SER A 201 " model vdw 2.296 3.040 nonbonded pdb=" NH1 ARG A 175 " pdb=" O LEU A 290 " model vdw 2.334 3.120 nonbonded pdb=" O VAL A 74 " pdb=" NH2 ARG A 113 " model vdw 2.385 3.120 nonbonded pdb=" OG1 THR A 245 " pdb=" OE1 GLU A 386 " model vdw 2.437 3.040 nonbonded pdb=" O ALA A 506 " pdb=" OG1 THR A 510 " model vdw 2.472 3.040 ... (remaining 28741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.800 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3642 Z= 0.176 Angle : 0.686 6.073 4969 Z= 0.391 Chirality : 0.039 0.165 574 Planarity : 0.027 0.651 613 Dihedral : 10.980 71.396 1265 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.38), residues: 452 helix: -0.84 (0.26), residues: 329 sheet: None (None), residues: 0 loop : 0.59 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 462 TYR 0.012 0.002 TYR A 168 PHE 0.032 0.002 PHE A 173 TRP 0.021 0.002 TRP A 288 HIS 0.003 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3639) covalent geometry : angle 0.68309 ( 4963) SS BOND : bond 0.00215 ( 3) SS BOND : angle 1.87409 ( 6) hydrogen bonds : bond 0.12882 ( 253) hydrogen bonds : angle 6.64435 ( 735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 132 SER cc_start: 0.8553 (p) cc_final: 0.8200 (m) REVERT: A 218 MET cc_start: 0.7252 (mmm) cc_final: 0.6998 (mmt) REVERT: A 346 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7634 (mtt90) REVERT: A 378 ASP cc_start: 0.7707 (m-30) cc_final: 0.7330 (m-30) REVERT: A 418 LEU cc_start: 0.8570 (tp) cc_final: 0.8242 (tp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0694 time to fit residues: 10.2930 Evaluate side-chains 86 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 115 HIS A 428 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.206873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.160328 restraints weight = 4625.836| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.80 r_work: 0.3790 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3642 Z= 0.139 Angle : 0.697 14.697 4969 Z= 0.334 Chirality : 0.040 0.219 574 Planarity : 0.005 0.075 613 Dihedral : 4.298 17.815 491 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 2.63 % Allowed : 10.79 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.42), residues: 452 helix: 1.23 (0.29), residues: 328 sheet: None (None), residues: 0 loop : 1.44 (0.66), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 488 TYR 0.010 0.001 TYR A 352 PHE 0.020 0.002 PHE A 22 TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 3639) covalent geometry : angle 0.69531 ( 4963) SS BOND : bond 0.00498 ( 3) SS BOND : angle 1.70398 ( 6) hydrogen bonds : bond 0.04377 ( 253) hydrogen bonds : angle 4.83699 ( 735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.138 Fit side-chains REVERT: A 22 PHE cc_start: 0.6487 (t80) cc_final: 0.6113 (t80) REVERT: A 121 CYS cc_start: 0.5688 (OUTLIER) cc_final: 0.5305 (m) REVERT: A 218 MET cc_start: 0.7636 (mmm) cc_final: 0.7291 (mmt) REVERT: A 227 PHE cc_start: 0.7960 (t80) cc_final: 0.7571 (t80) REVERT: A 346 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7614 (mtt90) REVERT: A 418 LEU cc_start: 0.8565 (tp) cc_final: 0.8254 (tp) outliers start: 10 outliers final: 6 residues processed: 94 average time/residue: 0.0586 time to fit residues: 6.9325 Evaluate side-chains 84 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 0.0570 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.204214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.158413 restraints weight = 4643.843| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.80 r_work: 0.3772 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3642 Z= 0.138 Angle : 0.665 14.397 4969 Z= 0.315 Chirality : 0.040 0.165 574 Planarity : 0.005 0.060 613 Dihedral : 4.129 17.272 491 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.89 % Allowed : 11.84 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.42), residues: 452 helix: 1.51 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.61 (0.67), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 402 TYR 0.012 0.001 TYR A 240 PHE 0.029 0.002 PHE A 22 TRP 0.012 0.001 TRP A 64 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3639) covalent geometry : angle 0.66395 ( 4963) SS BOND : bond 0.00888 ( 3) SS BOND : angle 1.39659 ( 6) hydrogen bonds : bond 0.04136 ( 253) hydrogen bonds : angle 4.64538 ( 735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5873 (OUTLIER) cc_final: 0.5514 (m) REVERT: A 218 MET cc_start: 0.7653 (mmm) cc_final: 0.7282 (mmt) REVERT: A 227 PHE cc_start: 0.8026 (t80) cc_final: 0.7706 (t80) REVERT: A 346 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7579 (mtt90) REVERT: A 418 LEU cc_start: 0.8571 (tp) cc_final: 0.8219 (tp) outliers start: 11 outliers final: 9 residues processed: 89 average time/residue: 0.0502 time to fit residues: 5.7462 Evaluate side-chains 89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 428 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.203851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.158358 restraints weight = 4655.185| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.78 r_work: 0.3762 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3642 Z= 0.132 Angle : 0.654 14.553 4969 Z= 0.307 Chirality : 0.040 0.192 574 Planarity : 0.004 0.051 613 Dihedral : 4.048 17.027 491 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 4.47 % Allowed : 11.58 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.43), residues: 452 helix: 1.72 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.67 (0.69), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 488 TYR 0.008 0.001 TYR A 352 PHE 0.033 0.002 PHE A 22 TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3639) covalent geometry : angle 0.65287 ( 4963) SS BOND : bond 0.00203 ( 3) SS BOND : angle 1.31877 ( 6) hydrogen bonds : bond 0.03949 ( 253) hydrogen bonds : angle 4.54007 ( 735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5917 (OUTLIER) cc_final: 0.5560 (m) REVERT: A 132 SER cc_start: 0.8775 (p) cc_final: 0.8451 (m) REVERT: A 218 MET cc_start: 0.7647 (mmm) cc_final: 0.7333 (mmt) REVERT: A 227 PHE cc_start: 0.8060 (t80) cc_final: 0.7744 (t80) REVERT: A 242 MET cc_start: 0.7336 (mtm) cc_final: 0.7015 (mtt) REVERT: A 346 ARG cc_start: 0.7987 (mtt180) cc_final: 0.7524 (mtt90) outliers start: 17 outliers final: 13 residues processed: 92 average time/residue: 0.0568 time to fit residues: 6.6433 Evaluate side-chains 94 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.0070 chunk 19 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.202797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.157416 restraints weight = 4565.795| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.74 r_work: 0.3732 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3642 Z= 0.128 Angle : 0.650 14.537 4969 Z= 0.306 Chirality : 0.039 0.155 574 Planarity : 0.004 0.045 613 Dihedral : 4.059 17.800 491 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.95 % Allowed : 13.16 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.43), residues: 452 helix: 1.82 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.58 (0.68), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 486 TYR 0.008 0.001 TYR A 352 PHE 0.026 0.001 PHE A 22 TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3639) covalent geometry : angle 0.64956 ( 4963) SS BOND : bond 0.00113 ( 3) SS BOND : angle 1.17052 ( 6) hydrogen bonds : bond 0.03915 ( 253) hydrogen bonds : angle 4.43586 ( 735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.079 Fit side-chains REVERT: A 121 CYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5569 (m) REVERT: A 218 MET cc_start: 0.7643 (mmm) cc_final: 0.7430 (mmt) REVERT: A 227 PHE cc_start: 0.8051 (t80) cc_final: 0.7717 (t80) REVERT: A 242 MET cc_start: 0.7310 (mtm) cc_final: 0.7011 (mtt) outliers start: 15 outliers final: 13 residues processed: 88 average time/residue: 0.0507 time to fit residues: 5.9073 Evaluate side-chains 92 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.2980 chunk 20 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.0370 chunk 6 optimal weight: 2.9990 overall best weight: 0.4260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.201967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.156378 restraints weight = 4643.555| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.76 r_work: 0.3713 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3642 Z= 0.121 Angle : 0.656 14.581 4969 Z= 0.304 Chirality : 0.039 0.166 574 Planarity : 0.004 0.040 613 Dihedral : 3.967 17.787 491 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.68 % Allowed : 15.26 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.43), residues: 452 helix: 1.95 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.48 (0.67), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.007 0.001 TYR A 352 PHE 0.026 0.001 PHE A 22 TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3639) covalent geometry : angle 0.65499 ( 4963) SS BOND : bond 0.00397 ( 3) SS BOND : angle 1.43841 ( 6) hydrogen bonds : bond 0.03689 ( 253) hydrogen bonds : angle 4.38576 ( 735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5891 (OUTLIER) cc_final: 0.5570 (m) REVERT: A 218 MET cc_start: 0.7676 (mmm) cc_final: 0.7435 (mmt) REVERT: A 242 MET cc_start: 0.7277 (mtm) cc_final: 0.7042 (mtt) REVERT: A 346 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7424 (mtt90) outliers start: 14 outliers final: 13 residues processed: 85 average time/residue: 0.0544 time to fit residues: 6.0107 Evaluate side-chains 88 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.0000 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.203964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.156894 restraints weight = 4743.667| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.89 r_work: 0.3716 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3642 Z= 0.124 Angle : 0.661 14.568 4969 Z= 0.306 Chirality : 0.039 0.192 574 Planarity : 0.004 0.040 613 Dihedral : 3.981 17.318 491 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.95 % Allowed : 16.58 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.43), residues: 452 helix: 1.95 (0.30), residues: 328 sheet: None (None), residues: 0 loop : 1.52 (0.67), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 486 TYR 0.009 0.001 TYR A 352 PHE 0.023 0.001 PHE A 22 TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3639) covalent geometry : angle 0.65983 ( 4963) SS BOND : bond 0.00173 ( 3) SS BOND : angle 1.24954 ( 6) hydrogen bonds : bond 0.03632 ( 253) hydrogen bonds : angle 4.40396 ( 735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5821 (OUTLIER) cc_final: 0.5512 (m) REVERT: A 218 MET cc_start: 0.7704 (mmm) cc_final: 0.7463 (mmt) REVERT: A 227 PHE cc_start: 0.8049 (t80) cc_final: 0.7673 (t80) REVERT: A 346 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7446 (mtt90) outliers start: 15 outliers final: 12 residues processed: 81 average time/residue: 0.0576 time to fit residues: 6.0587 Evaluate side-chains 87 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 8.9990 chunk 24 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 7 optimal weight: 0.0970 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.203156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156732 restraints weight = 4780.450| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.89 r_work: 0.3704 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3642 Z= 0.128 Angle : 0.681 14.555 4969 Z= 0.313 Chirality : 0.040 0.202 574 Planarity : 0.004 0.039 613 Dihedral : 3.975 17.413 491 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.68 % Allowed : 16.05 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.43), residues: 452 helix: 1.94 (0.30), residues: 328 sheet: None (None), residues: 0 loop : 1.52 (0.68), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 488 TYR 0.011 0.001 TYR A 352 PHE 0.021 0.001 PHE A 22 TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3639) covalent geometry : angle 0.68022 ( 4963) SS BOND : bond 0.00178 ( 3) SS BOND : angle 1.21296 ( 6) hydrogen bonds : bond 0.03631 ( 253) hydrogen bonds : angle 4.40343 ( 735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5833 (OUTLIER) cc_final: 0.5536 (m) REVERT: A 218 MET cc_start: 0.7710 (mmm) cc_final: 0.7465 (mmt) REVERT: A 227 PHE cc_start: 0.8011 (t80) cc_final: 0.7628 (t80) REVERT: A 378 ASP cc_start: 0.7903 (t0) cc_final: 0.7458 (m-30) REVERT: A 486 ARG cc_start: 0.7831 (mmp80) cc_final: 0.7492 (mmm160) outliers start: 14 outliers final: 13 residues processed: 85 average time/residue: 0.0551 time to fit residues: 6.1324 Evaluate side-chains 87 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.203457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157113 restraints weight = 4701.191| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.88 r_work: 0.3718 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3642 Z= 0.127 Angle : 0.683 14.572 4969 Z= 0.315 Chirality : 0.040 0.219 574 Planarity : 0.004 0.038 613 Dihedral : 3.980 17.033 491 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.68 % Allowed : 17.89 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.42), residues: 452 helix: 1.96 (0.30), residues: 322 sheet: None (None), residues: 0 loop : 1.47 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 488 TYR 0.017 0.001 TYR A 256 PHE 0.021 0.001 PHE A 348 TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3639) covalent geometry : angle 0.68213 ( 4963) SS BOND : bond 0.00153 ( 3) SS BOND : angle 1.14395 ( 6) hydrogen bonds : bond 0.03561 ( 253) hydrogen bonds : angle 4.46059 ( 735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5829 (OUTLIER) cc_final: 0.5523 (m) REVERT: A 227 PHE cc_start: 0.7995 (t80) cc_final: 0.7607 (t80) REVERT: A 378 ASP cc_start: 0.7921 (t0) cc_final: 0.7511 (m-30) REVERT: A 486 ARG cc_start: 0.7843 (mmp80) cc_final: 0.7501 (mmm160) outliers start: 14 outliers final: 13 residues processed: 82 average time/residue: 0.0494 time to fit residues: 5.4135 Evaluate side-chains 91 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 39 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.202379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.155890 restraints weight = 4775.714| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.91 r_work: 0.3711 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3642 Z= 0.130 Angle : 0.698 14.565 4969 Z= 0.320 Chirality : 0.040 0.224 574 Planarity : 0.004 0.034 613 Dihedral : 3.951 16.799 491 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.68 % Allowed : 18.68 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.42), residues: 452 helix: 1.94 (0.30), residues: 321 sheet: None (None), residues: 0 loop : 1.42 (0.64), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.009 0.001 TYR A 352 PHE 0.019 0.001 PHE A 348 TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3639) covalent geometry : angle 0.69755 ( 4963) SS BOND : bond 0.00166 ( 3) SS BOND : angle 1.19336 ( 6) hydrogen bonds : bond 0.03646 ( 253) hydrogen bonds : angle 4.50347 ( 735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5796 (OUTLIER) cc_final: 0.5480 (m) REVERT: A 227 PHE cc_start: 0.7983 (t80) cc_final: 0.7596 (t80) REVERT: A 378 ASP cc_start: 0.7925 (t0) cc_final: 0.7513 (m-30) outliers start: 14 outliers final: 13 residues processed: 86 average time/residue: 0.0459 time to fit residues: 5.2956 Evaluate side-chains 89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 2 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.0570 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.201810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.156499 restraints weight = 4694.803| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.72 r_work: 0.3717 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3642 Z= 0.132 Angle : 0.706 14.559 4969 Z= 0.324 Chirality : 0.041 0.218 574 Planarity : 0.004 0.035 613 Dihedral : 3.940 16.786 491 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.42 % Allowed : 18.95 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.42), residues: 452 helix: 1.91 (0.30), residues: 321 sheet: None (None), residues: 0 loop : 1.45 (0.63), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.017 0.001 TYR A 256 PHE 0.021 0.001 PHE A 348 TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3639) covalent geometry : angle 0.70553 ( 4963) SS BOND : bond 0.00160 ( 3) SS BOND : angle 1.17646 ( 6) hydrogen bonds : bond 0.03663 ( 253) hydrogen bonds : angle 4.53369 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1076.61 seconds wall clock time: 19 minutes 10.72 seconds (1150.72 seconds total)